Formation and dissociation of protonated cytosine–cytosine base pairs in i-motifs by ab initio quantum chemical calculations

doi:10.1088/1674-1056/23/2/020702

Abstract Formation and dissociation mechanisms of C–C⁺ base pairs in acidic and alkaline environments are investigated, employing ab initio quantum chemical calculations. Our calculations suggest that, in an acidic environment, a cytosine monomer is first protonated and then dimerized with an unprotonated cytosine monomer to form a C–C⁺ base pair; in an alkaline environment, a protonated cytosine dimer is first unprotonated and then dissociated into two cytosine monomers. In addition, the force for detaching a C–C⁺ base pair was found to be inversely proportional to the distance between the two cytosine monomers. These results provide a microscopic mechanism to qualitatively explain the experimentally observed reversible formation and dissociation of i-motifs.

Keywords: ab initio quantum chemical calculation i-motif protonated cytosine–cytosine base pair

Received: 22 September 2013
Revised: 17 October 2013
Accepted manuscript online:

PACS:	07.05.Tp	(Computer modeling and simulation)
	87.15.A-	(Theory, modeling, and computer simulation)
	87.15.-v	(Biomolecules: structure and physical properties)

Corresponding Authors: Wang Yan-Ting
E-mail: wangyt@itp.ac.cn

About author: 07.05.Tp; 87.15.A-; 87.15.-v

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Zhang Xiao-Hu (张小虎), Li Ming (黎明), Wang Yan-Ting (王延颋), Ouyang Zhong-Can (欧阳钟灿) Formation and dissociation of protonated cytosine–cytosine base pairs in i-motifs by ab initio quantum chemical calculations 2014 Chin. Phys. B 23 020702

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[1]	Mechano-chemical selections of two competitive unfolding pathways of a single DNA i-motif Xu Yue (徐悦), Chen Hu (陈虎), Qu Yu-Jie (璩玉杰), Artem K. Efremov, Li Ming (黎明), Ouyang Zhong-Can(欧阳钟灿) , Liu Dong-Sheng(刘冬生), Yan Jie (严洁). Chin. Phys. B, 2014, 23(6): 068702.

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Formation and dissociation of protonated cytosine–cytosine base pairs in i-motifs by ab initio quantum chemical calculations

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